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from __future__ import division, print_function
import numpy as np
from menpo.image import Image
from menpo.fitmultilevel.builder import DeformableModelBuilder
from menpo.fitmultilevel.functions import build_sampling_grid
from menpo.fitmultilevel.featurefunctions import compute_features, sparse_hog
from .classifierfu... | jabooth/menpo-archive | menpo/fitmultilevel/clm/builder.py | Python | bsd-3-clause | 17,337 | [
"Gaussian"
] | 8e6eeccc5ecb9ff051449f1260aa12abefb9d1b10a75f59f605b80e8e7779335 |
"""Loads configurations from .yaml files and expands environment variables.
"""
import copy
import collections
import glob
import math
import os
import pprint
import sys
import yaml
import toolz as tz
class CmdNotFound(Exception):
pass
# ## Generalized configuration
def update_w_custom(config, lane_info):
"... | mjafin/bcbio-nextgen | bcbio/pipeline/config_utils.py | Python | mit | 17,799 | [
"Bioconda",
"Galaxy"
] | 51f54bce9d3bc477302abf2759cb18bfdfde93d8731df2a25bef8965d4ba3742 |
# Custom library
import data_reader
# Standard libraries
import datetime
import os
import sys
import time
# Third-party libraries
import numpy as np
import tensorflow as tf
sess = tf.InteractiveSession()
# Short form of Boolean value
T, F = True, False
# Training/ classification setting ---------------------------... | kchng/Quantum_machine_learning | TF_HSF_CNN1.py | Python | apache-2.0 | 24,088 | [
"NEURON"
] | fe9438f31938e1f220593cb04087c91b7991e0b347ac0f04ed9476cf9d9b4601 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2016, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Unit tests for writer cjsonwriter module."""
import os
import unittest
import json
import cclib
__filedir__ = os.pa... | Schamnad/cclib | test/io/testcjsonwriter.py | Python | bsd-3-clause | 1,509 | [
"ADF",
"cclib"
] | cdffb3078c9b175839fcd5f47b4f0d5b9e8f667ee5bedd71ee7eefccf080fe85 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/utils/Platform/generic/generic_GetGatewayV6.py | Python | gpl-3.0 | 1,463 | [
"ORCA"
] | 0014e4a56e5db8eba86cf6cb4b94bbe63652cbc644d442b0d68ad49bb815b3ba |
"""
Module for support V_sim ascii fileformat
Contains routines to load .ascii files and
create pychemia Structure objects and to save
back to .ascii files
This code was originally created for ASE
"""
import re as _re
from pychemia.utils.constants import bohr_angstrom
from pychemia.core import Structure
def load(fi... | MaterialsDiscovery/PyChemia | pychemia/io/ascii.py | Python | mit | 6,387 | [
"ASE"
] | afa804a022dc296d0a95fdb513039676d1a18563fbe5c40c975d233c6e3772eb |
import pkg_resources
import sys
if sys.version_info < (3, 6):
raise EnvironmentError('Hail requires Python 3.6 or later, found {}.{}'.format(
sys.version_info.major, sys.version_info.minor))
__pip_version__ = pkg_resources.resource_string(__name__, 'hail_pip_version').decode().strip()
del pkg_resources
de... | danking/hail | hail/python/hail/__init__.py | Python | mit | 3,244 | [
"VisIt"
] | aef09b9a6fbf9db4d51d7972835b109a33b78904c57b53d32af49df86e5c276e |
#!/usr/bin/python
# -*- coding: utf-8 -*-
DOCUMENTATION = '''
---
version_added: "1.2"
module: jabber
short_description: Send a message to jabber user or chat room
description:
- Send a message to jabber
options:
user:
description:
User as which to connect
required: true
password:
description:... | hostmaster/ansible-modules-extras | notification/jabber.py | Python | gpl-3.0 | 3,778 | [
"Brian"
] | f58b093a39e19c71790fb92aca9f7d6eb2ca467ff502d08531444ffa8cb15f07 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | Stargrazer82301/CAAPR | CAAPR/CAAPR_AstroMagic/PTS/pts/do/fitskirt/psf.py | Python | mit | 5,502 | [
"Gaussian"
] | 34409cbfe0fe33d55cc018a28d87f6aeef2601626b095cfaab13af77b3601264 |
#!/usr/bin/env python
#
# Wrapper script for starting the biopet-vcfstats JAR package
#
# This script is written for use with the Conda package manager and is copied
# from the peptide-shaker wrapper. Only the parameters are changed.
# (https://github.com/bioconda/bioconda-recipes/blob/master/recipes/peptide-shaker/pep... | joachimwolff/bioconda-recipes | recipes/biopet-vcfstats/1.0/biopet-vcfstats.py | Python | mit | 3,367 | [
"Bioconda"
] | af6ded4a66e1447f6cbd559ee73895b7ecb9fa6d5187f2598d9e531add774784 |
"""XOR Neural Net."""
import numpy as np
def sigmoid(x):
"""The Sigmoid Function."""
return 1 / (1 + np.exp(-x))
def NOT(x):
"""OR Neuron."""
fx = 10 - 20 * x
return sigmoid(fx)
def AND(x1, x2):
"""AND Neuron."""
fx = 20 * x1 + 20 * x2 - 30
return sigmoid(fx)
def OR(x1, x2):
... | rednithin/Misc-Mini | DeepLearning/XORNeuralNet.py | Python | gpl-3.0 | 643 | [
"NEURON"
] | 5250cce688429c5fbf6f2a71cc312e1636ca9270d8c067f6c468c9754bd498f3 |
#!/usr/bin/env
"""
NARRuv_quiver_plot.py
"""
#System Stack
import datetime, sys
#Science Stack
from netCDF4 import Dataset, num2date
import numpy as np
# Visual Stack
import matplotlib as mpl
import matplotlib.pyplot as plt
from matplotlib.dates import MonthLocator, DateFormatter
import matplotlib.ticker as ticke... | shaunwbell/FOCI_Analysis | general_plotting_routines/uv_quiver_plot.py | Python | mit | 5,738 | [
"NetCDF"
] | 9c3494f3bc1c70ec8c9412b3ce3bc5e72be82506745ae1a0cf0293f18ded9825 |
# Copyright 2013 the V8 project authors. All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditi... | KSanthanam/rethinkdb | external/v8_3.30.33.16/test/benchmarks/testcfg.py | Python | agpl-3.0 | 7,349 | [
"Gaussian"
] | 92e5430202664a881bb94a9ddae3b333313d6fe74f2811825ff36df8debc0505 |
# -*- coding: utf-8 -*-
"""
Generators for geometric graphs.
"""
# Copyright (C) 2004-2011 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
__author__ = "\n".join(['Aric Hagberg (hagberg@lanl.gov)',
... | aitoralmeida/networkx | networkx/generators/geometric.py | Python | bsd-3-clause | 11,379 | [
"Gaussian"
] | acb1d7ca6ead522a76da6365b1e4774ad48f61663461ea7db309cb5a70bf2e40 |
#!/usr/bin/env python
import os
import sys
import subprocess as sp
import argparse
if sys.version_info.major == 3:
PY3 = True
from urllib.request import urlretrieve
else:
PY3 = True
from urllib import urlretrieve
usage = """
The easy way to test recipes is by using `circleci build`. However this doe... | ostrokach/bioconda-recipes | bootstrap.py | Python | mit | 4,385 | [
"Bioconda"
] | a7158b7c80f20662bfac390ac79fe8513dd0fa3164031fe0716444735f2dd2bb |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.community.HPBladeChassis | ZenPacks/community/HPBladeChassis/parsers/HPBladeChassis/EnclosureStatus.py | Python | gpl-2.0 | 3,122 | [
"VisIt"
] | 4acd9a6bbac7f3da05ff5f847074d37cdd816df587c82b60a1abb59836d4ea08 |
from __future__ import absolute_import # Need to import pulsar_client absolutely.
from ..objectstore import ObjectStore
from pulsar.client.manager import ObjectStoreClientManager
class PulsarObjectStore(ObjectStore):
"""
Object store implementation that delegates to a remote Pulsar server.
This may be m... | ssorgatem/pulsar | galaxy/objectstore/pulsar.py | Python | apache-2.0 | 2,899 | [
"Galaxy"
] | 1d525388b6cf9e35e4abff59868e30aa9d7eb4be795038056fe585cec2e809fa |
import os
import zipfile
import io
from django.views.generic import View, ListView, CreateView, UpdateView, DeleteView, DetailView
from django.shortcuts import render, render_to_response, get_object_or_404
from django.contrib.auth import authenticate, login, logout
from django.contrib.auth.models import Group, User
fro... | mgstigler/cs3240-s15-team19 | secure_witness/views.py | Python | mit | 24,658 | [
"VisIt"
] | 3e2f99ffa3ab5b04b8a90ae045789b2097cc7620d3f7dd8492554b93f1cfdf15 |
'''
Simple metropolis sampler class
'''
import numpy as np
np.random.seed(0)
def Metropolis(n_samples, fun_calcLLK, fun_verify, data, m_ini, prior_bounds,
prop_cov):
'''
Metropolis algorithm
Args:
* n_samples: Number of samples
* fun_calcLLK: Function to calculate Log-lik... | amaggi/am_bayes | teaching_eqloc/Metropolis.py | Python | gpl-2.0 | 1,767 | [
"Gaussian"
] | 9619a04dd8c6192560ea0a74b41d061a9d74dd9b359f54484ac24598cbb26b4f |
# Copyright (c) 2006-2013 Regents of the University of Minnesota.
# For licensing terms, see the file LICENSE.
import copy
import datetime
from lxml import etree
import os
import psycopg2
import sys
import time
import traceback
import uuid
import conf
import g
from grax.access_level import Access_Level
from grax.acc... | lbouma/Cyclopath | pyserver/item/feat/route.py | Python | apache-2.0 | 99,604 | [
"VisIt"
] | 3aabebf13a6a62ea299acae7e5af2b514a8b0f0f5f2bf8c2345bf25fcb0e08fb |
#!/usr/bin/env python
# coding=utf-8
from distutils.core import setup
from setuptools import find_packages
PACKAGE = "lightnn"
NAME = "lightnn"
DESCRIPTION = "This package can download funds data from https://github.com/l11x0m7/lightnn. For details, please visit https://skyhigh233.com."
AUTHOR = "Xuming Lin"... | l11x0m7/lightnn | setup.py | Python | apache-2.0 | 1,091 | [
"VisIt"
] | edb16622c8c45efbb4c71c87f4aaed938c32a8353a66376640334eed9a450418 |
"""
Implements various interpreters and modders for VASP.
"""
from pymatgen.io.vasp.inputs import VaspInput
from custodian.ansible.actions import DictActions, FileActions
from custodian.ansible.interpreter import Modder
class VaspModder(Modder):
"""
A Modder for VaspInputSets.
"""
def __init__(self... | materialsproject/custodian | custodian/vasp/interpreter.py | Python | mit | 2,115 | [
"VASP",
"pymatgen"
] | 2ad64553bc1cf0fa1ff3d24f2008f6dcd254dda17321b29fa3d9728ffd36afd3 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
dimensions= 1
size1d = 30
halfSize1 = [size1d,0.2,0.1]
halfSize2 = halfSize1
GRIDSIZE = 256
# wavepacket parameters
k0_x = 0
k0_y = 0
gaussWidth_x = 1.0
gaussWidth_y = 0.0
potentialCoefficient1= [-2.0,0.5,0.5]
potentialCoefficient2= [ 2.0,0.5,0.5]
O.engin... | cosurgi/trunk | examples/qm/1d-coulomb-interaction.py | Python | gpl-2.0 | 7,851 | [
"Gaussian"
] | cda8bab9ff0bcb348eb061d10160a95c22aa59b931ef1b814292a15b310d2e0d |
# -*- coding: utf-8 -*-
"""
======================
Laplacian segmentation
======================
This notebook implements the laplacian segmentation method of
`McFee and Ellis, 2014 <http://bmcfee.github.io/papers/ismir2014_spectral.pdf>`_,
with a couple of minor stability improvements.
Throughout the example, we wil... | bmcfee/librosa | docs/examples/plot_segmentation.py | Python | isc | 8,172 | [
"Brian"
] | a4530b2b1747d39e254603743b8ff712f65f6b48514017c7e06af13019180cf4 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2002-2017 Prof. William H. Green (whgreen@mit.edu),
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu)
#
# ... | Molecular-Image-Recognition/Molecular-Image-Recognition | code/rmgpy/data/base.py | Python | mit | 57,065 | [
"RDKit"
] | f458901395cad966d7de67762691665005b2830c8f9a5c5fec12be16781f722d |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string, optparse, subprocess
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','desc... | titanium-forks/testfairy.ti.testfairy | build.py | Python | apache-2.0 | 8,789 | [
"VisIt"
] | 10bda057c491378583833d6a7c77f15c495bd2c3f362512b9bd35a90c46e7714 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2013 Radim Rehurek <me@radimrehurek.com>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""
Deep learning via word2vec's "skip-gram and CBOW models", using either
hierarchical softmax or negative sampling [1]_ [2]_.
The train... | zclfly/gensim | gensim/models/word2vec.py | Python | gpl-3.0 | 81,199 | [
"VisIt"
] | 8b7c19148254812b6cd9d15650722eebf28681c3e20965fd5963b5bda924a759 |
# mako/parsetree.py
# Copyright 2006-2021 the Mako authors and contributors <see AUTHORS file>
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""defines the parse tree components for Mako templates."""
import re
from mako import ast
from ma... | sqlalchemy/mako | mako/parsetree.py | Python | mit | 19,007 | [
"VisIt"
] | e1243dadd7cdbd74bedea66f6f5703f0a5925f21091a110a73d4af35fcb8a286 |
# coding: utf-8
'''
-----------------------------------------------------------------------------
Copyright 2015 Esri
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses... | jfrygeo/solutions-geoprocessing-toolbox | suitability/toolboxes/scripts/DeleteOldFiles.py | Python | apache-2.0 | 2,088 | [
"NetCDF"
] | e6b60e90d772582635e22cfdc61571650ced7afa77927e23bec852d51f03ab68 |
from ase import Atom
from ase.units import Hartree
from gpaw import GPAW, FermiDirac
from gpaw.cluster import Cluster
from gpaw.test import equal
h =.3
box = 4.
energy_tolerance = 0.0004
l=2 # d-orbitals
U_ev=3 # U in eV
U_au=U_ev / Hartree # U in atomic units
scale=1 ... | qsnake/gpaw | gpaw/test/Hubbard_U_Zn.py | Python | gpl-3.0 | 975 | [
"ASE",
"GPAW"
] | fd9fa1bebf72599b9b29f4448a2758252d81358e189ec780bcd18f9ed15ed212 |
"""A medical image analysis pipeline.
The pipeline is used for brain tissue segmentation using a decision forest classifier.
"""
import argparse
import datetime
import os
import sys
import timeit
import SimpleITK as sitk
import numpy as np
from tensorflow.python.platform import app
from sklearn.mixture import Gaussia... | mrunibe/MIALab | bin/main_GMM.py | Python | apache-2.0 | 9,906 | [
"Gaussian"
] | 1d0008f0ba2280ac08482873e48a8a1229920db29051f7da281ebe2dcd0c416b |
# coding=utf-8
#-------------------------------------------------------------------------------
#Author: Alexandre Manhaes Savio <alexsavio@gmail.com>
#Grupo de Inteligencia Computational <www.ehu.es/ccwintco>
#Universidad del Pais Vasco UPV/EHU
#
#2013, Alexandre Manhaes Savio
#Use this at your own risk!
#-----------... | Neurita/cajal | cajal/render.py | Python | bsd-3-clause | 22,297 | [
"Mayavi"
] | 56c8bc440867dfd1bd580566476479853b07085bd0958bd7e6b8dd08a9b02e25 |
# coding=utf-8
"""Helper functions for optimal_tree pipeline."""
from __future__ import division
import ast
from decimal import Decimal
import errno
import math
import os
import pandas
from sklearn.feature_extraction import DictVectorizer
def make_dirs(path):
"""Recursively make directories, ignoring when they al... | PandaStabber/Goldberg_et_al_2016 | helper_functions.py | Python | mit | 17,341 | [
"Avogadro"
] | 30af7da846590ac0c4104ab06dbb20c6c8576d47badcbde8f2b3962b276f251c |
# -*- coding: UTF-8 -*-
"""Takes an arbitrary slice of the input data using an implicit cut
plane and warps it according to the vector field data. The scalars
are displayed on the warped surface as colors.
"""
# Authors: Fr�d�ric Petit and Prabhu Ramachandran
# Copyright (c) 2006, Enthought, Inc.
# License: BSD Style... | dmsurti/mayavi | mayavi/modules/warp_vector_cut_plane.py | Python | bsd-3-clause | 7,380 | [
"Mayavi",
"VTK"
] | 66d1ddf6787916ab1c6896b4605be53b20ac7249eab1380a1e6860e0112b07d2 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2016, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License... | dmillington/ansible-modules-core | system/systemd.py | Python | gpl-3.0 | 15,510 | [
"Brian"
] | 3c2785c54729cb9049fd8ade0838fda4830549cf10723f21f605a35d41f8b3f1 |
"""
Job Base Class
This class provides generic job definition functionality suitable for any VO.
Helper functions are documented with example usage for the DIRAC API. An example
script (for a simple executable) would be::
from DIRAC.Interfaces.API.Dirac import Dirac
from DIRAC.Interfaces.API.J... | marcelovilaca/DIRAC | Interfaces/API/Job.py | Python | gpl-3.0 | 47,518 | [
"DIRAC"
] | 10cf6c9f457d466929460586a9ca9ad8a30a31e0e3a7ecf656ae1730ce9f11d2 |
# Orca
#
# Copyright 2008-2009 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/packagemanager/tutorialgenerator.py | Python | gpl-3.0 | 2,744 | [
"ORCA"
] | 0fff3e280188d3d4bc7a9e5eea8182036b1fb6ec5171abcf3e6be5bf778b538b |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | andysim/psi4 | doc/sphinxman/source/psi4doc/__init__.py | Python | gpl-2.0 | 1,500 | [
"Psi4"
] | d86fec54ab6d7fa09ec1f840a207620850e2f97d81cbcb58cc16cc7a2b88f633 |
"""
Copyright (c) 2016 Jet Propulsion Laboratory,
California Institute of Technology. All rights reserved
"""
import logging
from calendar import timegm, monthrange
from datetime import datetime
import numpy as np
from nexustiles.nexustiles import NexusTileService
from webservice.NexusHandler import nexus_handler, S... | dataplumber/nexus | analysis/webservice/algorithms_spark/ClimMapSpark.py | Python | apache-2.0 | 12,964 | [
"NetCDF"
] | dd2669fedd86100faa89dde1f11d61c6ebed7a18cf90bec882477aa53598fd58 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# kernel_test - tests some kernel functions in standalone mode
# Copyright (C) 2003-2011 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the ... | heromod/migrid | mig/grsfs-fuse/fs/kernel_test.py | Python | gpl-2.0 | 4,109 | [
"Brian"
] | 3605819ee730a789e3b6dfcfdee26e1c0fdac3b8d43922589e69ff6c9fd9580a |
## Copyright 2016 Kurt Cutajar, Edwin V. Bonilla, Pietro Michiardi, Maurizio Filippone
##
## Licensed under the Apache License, Version 2.0 (the "License");
## you may not use this file except in compliance with the License.
## You may obtain a copy of the License at
##
## http://www.apache.org/licenses/LICENSE-2.0... | mauriziofilippone/deep_gp_random_features | code/utils.py | Python | apache-2.0 | 5,184 | [
"Gaussian"
] | 07ab729a1c1b429ff8920f324878cc4af1794ea4bb833d52fc9d895eaeaec21d |
import sys, os, inspect
import os, sys, inspect, inviwopy
path_to_current_folder = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
sys.path.append(path_to_current_folder + "/../")
import envisionpy
import envisionpy.hdf5parser
from envisionpy.network import VisualisationManager
# Path to the ... | rartino/ENVISIoN | demo/parchg.py | Python | bsd-2-clause | 844 | [
"VASP"
] | 6c6aa1fb6063eb77ea713a7e58cb16971a07fd1d7b2347eaf747e612a205f6c4 |
# -*- coding: utf-8 -*-
"""
This file contains settings required to make ICs for the dust settling test
of Price & Laibe (2015) (see section 4.4 Dust settling in a protoplanetary disc)
This uses a stretched cubic grid with a gaussian vertical density profile as
a starting point (similar to Price & Laibe's hexagonal gri... | ibackus/testdust | src/examples/settling-ICgen/settings_hexagonal.py | Python | mit | 2,001 | [
"Gaussian"
] | f969d380861cabef1f8585b885116033fabc7ddd6b9954f66f4df60391acaffe |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | hmenke/espresso | samples/constraints.py | Python | gpl-3.0 | 4,048 | [
"ESPResSo"
] | 36a488bd5ee8aa6a8c8e786e6518c925112c4a93646838a8ea700ed09d84438f |
from __future__ import absolute_import
from __future__ import print_function
import glob
import os, sys
from datetime import datetime, timedelta
import logging
log = logging.getLogger(__name__)
log.addHandler(logging.NullHandler())
import numpy as np
from .density_to_files import (accumulate_points_on_grid,
accu... | deeplycloudy/lmatools | lmatools/grid/make_grids.py | Python | bsd-2-clause | 31,955 | [
"NetCDF"
] | 95a5467961712e9dc67c865d3d6f9265d10b3f4febe43cd32000ade8acd5950d |
# This file is part of BHMM (Bayesian Hidden Markov Models).
#
# Copyright (c) 2016 Frank Noe (Freie Universitaet Berlin)
# and John D. Chodera (Memorial Sloan-Kettering Cancer Center, New York)
#
# BHMM is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public Licen... | jchodera/bhmm | bhmm/hmm/discrete_hmm.py | Python | lgpl-3.0 | 3,417 | [
"Gaussian"
] | 81d28d8b33685670517b2cc375e9be7aee18609eac805514cd2a0da0ab82d2c6 |
#!/usr/bin/env python
"""
Restart DIRAC component using runsvctrl utility
"""
__RCSID__ = "$Id$"
#
from DIRAC.Core.Base import Script
Script.disableCS()
Script.setUsageMessage('\n'.join([__doc__.split('\n')[1],
'Usage:',
' %s [option|cfgfile] ... [S... | andresailer/DIRAC | FrameworkSystem/scripts/dirac-restart-component.py | Python | gpl-3.0 | 1,178 | [
"DIRAC"
] | 1849798b4ac541bef98b76240f0bf7aebc9b4043db30090463db9a15467c3039 |
"""Script to download or update SIMBAD-related databases"""
__author__ = "Felix Simkovic & Adam Simpkin"
__date__ = "17 May 2017"
__version__ = "1.0"
import argparse
import collections
import datetime
import glob
import json
import numpy as np
import pandas as pd
import morda
import os
import shutil
import ssl
import... | rigdenlab/SIMBAD | simbad/command_line/simbad_database.py | Python | bsd-3-clause | 33,539 | [
"CRYSTAL"
] | 416da75f67d6b21d52e1616322fbcec9e8ee941f5b19a8ee06c5743c803a5079 |
# destiny_Wrapper/destiny_Wrapper.py - a self annotated version of rgToolFactory.py generated by running rgToolFactory.py
# to make a new Galaxy tool called destiny_Wrapper
# User admin@galaxy.org at 19/08/2015 09:31:41
# rgToolFactory.py
# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
#
# copyright ross... | myoshimura080822/tools_of_rnaseq_on_docker_galaxy | destiny_Wrapper/destiny_Wrapper.py | Python | mit | 32,902 | [
"Galaxy"
] | 8c83fede97b77c718e38977ae520031e57dfab8ca3648fbc37dda49e159f4e81 |
import copy
# flake8: noqa
LSPCI = """
0000:00:00.0 "Host bridge" "Intel Corporation" "Haswell-E DMI2" -r02 "Intel Corporation" "Device 0000"
0000:00:03.0 "PCI bridge" "Intel Corporation" "Haswell-E PCI Express Root Port 3" -r02 "" ""
0000:00:03.2 "PCI bridge" "Intel Corporation" "Haswell-E PCI Express Root Port 3" -r0... | coreycb/charms.openstack | unit_tests/pci_responses.py | Python | apache-2.0 | 10,045 | [
"ORCA"
] | d7419981a29e65332417c38b7b07479af47b337987e912401b6ad260ef75c36a |
import sys
from mpi4py import MPI
import numpy as np
from delight.io import *
from delight.utils import *
from delight.photoz_gp import PhotozGP
from delight.photoz_kernels import Photoz_mean_function, Photoz_kernel
from delight.utils_cy import approx_flux_likelihood_cy
# Parse parameters file
if len(sys.argv) < 2:
... | ixkael/Delight | scripts/delight-optimize.py | Python | mit | 9,708 | [
"Galaxy"
] | 7ff608535b4ff5d848fe272447bbb95974ceb16699acd983001000bb7380d697 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
################################################################################
#
# qooxdoo - the new era of web development
#
# http://qooxdoo.org
#
# Copyright:
# 2006-2013 1&1 Internet AG, Germany, http://www.1und1.de
#
# License:
# LGPL: http://www.gnu.org/li... | sebastienhupin/qxrad | qooxdoo/tool/pylib/ecmascript/transform/moztree_to_tree1.py | Python | lgpl-3.0 | 21,023 | [
"VisIt"
] | 98f9044e89b049165ac0c6605ab1a439763bc1e184cafcd549a64ccd1de7d510 |
import numpy as np
from gpaw.overlap import Overlap
from gpaw.fd_operators import Laplace
from gpaw.lfc import LocalizedFunctionsCollection as LFC
from gpaw.utilities import unpack
from gpaw.io import FileReference
from gpaw.lfc import BasisFunctions
from gpaw.utilities.blas import axpy
from gpaw.transformers import T... | ajylee/gpaw-rtxs | gpaw/wavefunctions/fd.py | Python | gpl-3.0 | 10,754 | [
"GPAW"
] | e3ee5c75e80d9277444d0d95ebc35014236ae280f93b56ad03426c7ee9b899ac |
# -----------------------------------------------------------------------------
# Copyright (c) 2014--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# -------------------------------------------... | JWDebelius/scikit-bio | skbio/alignment/_ssw/__init__.py | Python | bsd-3-clause | 628 | [
"scikit-bio"
] | d55c5fa9fd005dc78232ae2ffdf2a691ce08a5a050c27c0e0a6539430382bffd |
"""
Histogram vs Kernel Density Estimation
--------------------------------------
Figure 6.1
Density estimation using histograms and kernels. The top panels show two
histogram representations of the same data (shown by plus signs in the bottom
of each panel) using the same bin width, but with the bin centers of the
hi... | eramirem/astroML | book_figures/chapter6/fig_hist_to_kernel.py | Python | bsd-2-clause | 4,774 | [
"Gaussian"
] | 0599c3be018b6e1b33f4dd8bfe87c23890ba81c83ef11d455f73da4288ff930e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2012 Jared Boone
#
# This file is part of HackRF.
#
# This is a free hardware design; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2, or (at your opt... | pavsa/hackrf-spectrum-analyzer | src/hackrf-sweep/lib/hackrf/hardware/test/si5351-configure.py | Python | gpl-3.0 | 6,337 | [
"CRYSTAL"
] | ab4720459622ba195c70a0883df772a32f4aa90278cb925832679736035be3f1 |
#!/usr/bin/env python
import os.path, sys
import tornado.auth
import tornado.httpserver
import tornado.ioloop
import tornado.options
import tornado.web
from tornado import gen
from tornado.web import asynchronous
from threading import Thread
from functools import wraps
import chancecoind
from lib import (config, util... | chancecoin/chancecoin | server.py | Python | mit | 18,659 | [
"CASINO"
] | d182eab6fc021407f6d9735e61ac0fd1ecbad8c4ff18fbb963aa478595e6c6c7 |
from django import forms
from django.contrib.admin.widgets import AdminRadioSelect, AdminRadioFieldRenderer
from edc_base.form.old_forms import BaseModelForm
from edc_constants.constants import ON_STUDY
from edc_visit_tracking.forms import VisitFormMixin
from tshilo_dikotla.choices import VISIT_REASON, VISIT_INFO_SOU... | botswana-harvard/tshilo-dikotla | td_infant/forms/infant_visit_form.py | Python | gpl-2.0 | 4,943 | [
"VisIt"
] | 8ba640934f29985b31b664e96ad7f86cd2284c5836474923e8b12e1fd626b038 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publish... | thica/ORCA-Remote | src/ORCA/utils/FileName.py | Python | gpl-3.0 | 7,486 | [
"ORCA"
] | 259f777ac8599dfc8857ba3ae4f7793a5d0ece9760c69a4b0d534d55e5d7a3c6 |
TEX = """
text here \citet{robitaille:08:2413}
more \cite{forbrich:10:1453} text
(\citealt{robitaille:06:256})
"""
EXPECTED = r"""
@ARTICLE{forbrich:10:1453,
author = {{Forbrich}, J. and {Tappe}, A. and {Robitaille}, T. and {Muench}, A.~A. and
{Teixeira}, P.~S. and {Lada}, E.~A. and {Stolte}, A. and {Lada}, C.~J.... | astrofrog/auto_bibtex | test_auto_bibtex.py | Python | mit | 2,663 | [
"Galaxy"
] | 286c4cb3d5ef50b1eb6cc6f9acff4b1d2d3d0526c14a5aff61659cc213dca686 |
from __future__ import absolute_import
from django.utils.translation import ugettext_lazy as _
from sentry import http, options
from sentry.identity.pipeline import IdentityProviderPipeline
from sentry.identity.github import get_user_info
from sentry.integrations import Integration, IntegrationFeatures, IntegrationPr... | looker/sentry | src/sentry/integrations/github/integration.py | Python | bsd-3-clause | 7,082 | [
"VisIt"
] | 1795a0ce0a2d94a27b4dddf4fb461dc7d64432a0aa4dfd0a82792d083e87e546 |
# PrequelPrizes server-side code Copyright (c) 2013 Chris Cogdon - chris@cogdon.org
import codecs
import csv
from uuid import uuid4
import hmac
import hashlib
import sys
import cStringIO
from django import forms
from django.contrib.auth.decorators import permission_required
from django.core.exceptions import Permissi... | chmarr/prequelprizes | prizes/views.py | Python | gpl-2.0 | 7,156 | [
"VisIt"
] | e38f46c3bb9f48f4e7ce8527e05334f35449c188848539262fdc3b1b503213bb |
# Python Imports
import datetime
# Rest Framework Imports
from rest_framework import serializers
from rest_framework import viewsets
from rest_framework.decorators import detail_route, list_route
from rest_framework.response import Response
#Local Imports
import contacts.models as cont
from messages import Participan... | tperrier/mwachx | contacts/serializers/visits.py | Python | apache-2.0 | 4,316 | [
"VisIt"
] | 21b3b11b2c81f8a0c6a26f9caea6fc853c78a8e2200fbf05b90c877c4dc7ce6d |
""" SiteInspectorAgent
This agent inspect Sites, and evaluates policies that apply.
The following options can be set for the SiteInspectorAgent.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN SiteInspectorAgent
:end-before: ##END
:dedent: 2
:caption: SiteInspectorAgent options
"""
__RCSID... | petricm/DIRAC | ResourceStatusSystem/Agent/SiteInspectorAgent.py | Python | gpl-3.0 | 5,884 | [
"DIRAC"
] | c4ae04d7bafe2e3a1d6fb29427c40b4564cc5333ea4b00ab809d64dd82147c17 |
#!/usr/bin/env python
"""
PyVTK provides tools for manipulating VTK files in Python.
VtkData - create VTK files from Python / read VTK files to Python
"""
"""
Copyright 2001 Pearu Peterson all rights reserved,
Pearu Peterson <pearu@ioc.ee>
Permission to use, modify, and distribute this software is... | ddempsey/PyFEHM | pyvtk/__init__.py | Python | lgpl-2.1 | 10,343 | [
"VTK"
] | 150457fcad793f101fbbb3d32eb14ba44161b9bcc5d7eefc8d8d96b402a63a92 |
#!/usr/bin/env python3
import arbor
import argparse
import numpy as np
import pandas
import seaborn # You may have to pip install these.
class Cable(arbor.recipe):
def __init__(self, probes,
Vm, length, radius, cm, rL, g,
stimulus_start, stimulus_duration, stimulus_amplitude,
... | halfflat/nestmc-proto | python/example/single_cell_cable.py | Python | bsd-3-clause | 7,141 | [
"NEURON"
] | ac45f37b64bacc78454aced5404677a428200c14e78dafbc384da85f427c0ccd |
import numpy
from trefoil.analysis.summary import summarize_areas_by_category, calculate_weighted_statistics
from trefoil.utilities.window import Window
# Days per month from Tim, starting with January. Useful for weighting statistics when rolling months up to year.
# Assumes 365 day calendar with no leap year... | consbio/clover | trefoil/analysis/timeseries.py | Python | bsd-3-clause | 5,913 | [
"NetCDF"
] | 759b5a0bb2e9a69cbc1990d1879f2588e4c8fc584bf9ace383b435349dd54214 |
"""User-friendly public interface to polynomial functions. """
from __future__ import print_function, division
from sympy.core import (
S, Basic, Expr, I, Integer, Add, Mul, Dummy, Tuple
)
from sympy.core.mul import _keep_coeff
from sympy.core.symbol import Symbol
from sympy.core.basic import preorder_traversal
... | sahilshekhawat/sympy | sympy/polys/polytools.py | Python | bsd-3-clause | 172,191 | [
"Gaussian"
] | e77e2f9ab8e6d1004f6873edd977c71cf6e7b55024804c3cea302bffc501612c |
# This file is part of Androguard.
#
# Copyright (C) 2014 Google Inc. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
... | kanpol/abugfinder | tools/modified/androguard/decompiler/dad/ast.py | Python | gpl-3.0 | 23,808 | [
"VisIt"
] | 2d151b71d65eff58c39e59a2f5ca5995f4b0252c643c3100d7dbfe0e8b1095c2 |
#
# Copyright (C) 2011-2021 Greg Landrum and other RDKit contributors
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
import base64
import copy
i... | rdkit/rdkit | rdkit/Chem/Draw/IPythonConsole.py | Python | bsd-3-clause | 12,511 | [
"RDKit"
] | 51d840e226799ce027df635792db3006f150e81652615a7a5ec99b68265f3f2e |
from setuptools import setup, find_packages
from pip.req import parse_requirements
install_reqs = parse_requirements('requirements.txt', session=False)
version = '0.2.5'
LONG_DESCRIPTION = """
=====
Zops
=====
Zops - Utils for devops teams that want to deploy using Zappa
"""
setup(
name='zops',
version=ve... | bjinwright/zops | setup.py | Python | gpl-3.0 | 1,042 | [
"Brian"
] | 5bb349830b4d3992a72ca6b28401944a94c475e3995b6eb84d8df705c6b1add8 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module contains classes to wrap Python VTK to make nice molecular plots.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, The Mate... | matk86/pymatgen | pymatgen/vis/structure_vtk.py | Python | mit | 47,013 | [
"Jmol",
"VTK",
"pymatgen"
] | 59014ea6d82d56f216371e645f45833f720d6b366f2e1240c3a3c271fae3ea81 |
#!BPY
"""
Name: 'Sunflow Exporter (.sc)...'
Blender: 2.4
Group: 'Export'
Tip: ''
"""
"""
Version : 0.07.0 (January 2007)
Author : R Lindsay (hayfever) / Christopher Kulla
Description : Export to Sunflow renderer http://sunflow.sourceforge.net/
"""
## imports ##... | Acbentle/terrain474 | exporters/blender/sunflow_export.py | Python | mit | 32,579 | [
"Gaussian"
] | c69c3f15c374e80d65e5d4ef815e7cfa317f98c1f4498d1d6abc67475704713e |
# python script, to extract circular reads from a bam file, based on a tab-separated circle_id - reads file and a bam file. writes out circle-specific bam files
# input: tab-separated file with circle id as chr:start-end\tlist with read names
# input: bamfile containing circle reads (as well as others)
# output: circ... | dieterich-lab/FUCHS | GCB_testset/FUCHS/extract_reads.py | Python | gpl-3.0 | 4,638 | [
"pysam"
] | 35cb6ce06464c9fec107664d0dba74e304ebbf83b1a76b19e0288cacbba8f3de |
"""
Test LogLevels module
"""
__RCSID__ = "$Id$"
import logging
import pytest
from DIRAC.FrameworkSystem.private.standardLogging.LogLevels import LogLevels
@pytest.mark.parametrize(
"logLevel, value",
[
("debug", logging.DEBUG),
("verbose", 15),
("info", 20),
("warn", loggin... | ic-hep/DIRAC | src/DIRAC/FrameworkSystem/private/standardLogging/test/Test_LogLevels.py | Python | gpl-3.0 | 1,351 | [
"DIRAC"
] | 78c417c72683219209aef22dfc07e6640c08678e79c7b0a3315d4a4b1f18e421 |
import vtk
red = [255, 0, 0]
green = [0, 255, 0]
blue = [0, 0, 255]
# Setup the colors array
colors = vtk.vtkUnsignedCharArray()
colors.SetNumberOfComponents(3)
colors.SetName("Colors")
# Add the colors we created to the colors array
colors.InsertNextTypedTuple(red)
colors.InsertNextTypedTuple(red)
colors.InsertNext... | tjssmy/CuviewerPy | vtkTests/All.py | Python | mit | 4,709 | [
"VTK"
] | ea715de5a46a09a384f377b6104c707f38ab8ab9aab42b468d83d142f97c5030 |
from chiplotle.geometry.core.group import Group
from chiplotle.geometry.core.path import Path
from chiplotle.geometry.core.coordinate import Coordinate
from chiplotle.geometry.core.coordinatearray import CoordinateArray
from chiplotle.geometry.transforms.transformvisitor import TransformVisitor
import random
def noise... | drepetto/chiplotle | chiplotle/geometry/transforms/noise.py | Python | gpl-3.0 | 1,251 | [
"VisIt"
] | b07544ef9ecd892d485cfb90a16b3d605eb878764d137e97d3c5c67c72407d0c |
"""
Copyright 2015 Hewlett-Packard
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, softwar... | szaher/freezer-api | freezer_api/storage/elastic.py | Python | apache-2.0 | 22,193 | [
"Elk"
] | 98d4800d8f3166f3bf8c0ae111cfafa8cb998c2cfd44528579c2c17cc2189789 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
#******************************************************************************
#*
#* Copyright (C) 2015 Kiran Karra <kiran.karra@gmail.com>
#*
#* This program is free software: you can redistribute it and/or modify
#* it under the terms of the GNU General Public Licens... | kkarrancsu/copula-bayesian-networks | invcopulastat.py | Python | gpl-3.0 | 5,492 | [
"Gaussian"
] | 4d3711af8fb1717a6908a7e04672297bba917cb4d6eac9203d58144ca3c189dc |
"""
It is used to compile the web framework
"""
import os
import tempfile
import shutil
import subprocess
import gzip
import sys
from DIRAC import gLogger, gConfig, rootPath, S_OK, S_ERROR
from DIRAC.Core.Utilities.CFG import CFG
__RCSID__ = "$Id$"
class WebAppCompiler(object):
def __init__(self, params):
... | andresailer/DIRAC | FrameworkSystem/Client/WebAppCompiler.py | Python | gpl-3.0 | 13,996 | [
"DIRAC"
] | e964183274100cee2163fc370de307adc809127d543792efb0fa86454bfcdb79 |
# -*- coding: utf-8 -*-
#
# multimeter_file.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License... | uahic/nest-simulator | pynest/examples/multimeter_file.py | Python | gpl-2.0 | 5,227 | [
"NEURON"
] | c8cc5e3f1c5abfea19b5fd3e4579ae0610e63325f6b16d8eac8927b36a0f6e52 |
#! /usr/bin/env python
########################################################################
# File : dirac-admin-bdii-info
# Author : Aresh Vedaee
########################################################################
"""
Check info on BDII for a given CE or site
"""
__RCSID__ = "$Id$"
import DIRAC
from DIR... | andresailer/DIRAC | ConfigurationSystem/scripts/dirac-admin-bdii-info.py | Python | gpl-3.0 | 4,570 | [
"DIRAC"
] | e162262e79dc1eef2751fba60e44afff66a4b9f915d50c2e9b031bf7baf1a017 |
#
# @file TestUnitDefinition.py
# @brief SBML UnitDefinition unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Ben Bornstein
#
# $Id$
# $HeadURL$
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automaticall... | alexholehouse/SBMLIntegrator | libsbml-5.0.0/src/bindings/python/test/sbml/TestUnitDefinition.py | Python | gpl-3.0 | 18,004 | [
"VisIt"
] | 99fb193b9b1a0a5bc8c69c0ebdd8a823699385960bfb886de3d0419faef11cff |
"""
Image processing routines
Most of these are specific to PyVoyager
"""
import os
import os.path
import scipy.ndimage as ndimage # n-dimensional images - for blob detection
import numpy as np
import cv2
import math
import random
import PIL
from PIL import Image
from PIL import ImageFont
from PIL import ImageDraw
... | bburns/PyVoyager | src/libimg.py | Python | mit | 52,860 | [
"Gaussian"
] | dba47f7f7a796f9b6d5493e4abd271b31de5d8f071f16203a75946fc761d7cd4 |
"""
The Job Sanity Agent accepts all jobs from the Job
receiver and screens them for the following problems:
- Output data already exists
- Problematic JDL
- Jobs with too much input data e.g. > 100 files
- Jobs with input data incorrectly specified e.g. castor:/
- Input sandbox not correc... | petricm/DIRAC | WorkloadManagementSystem/Executor/JobSanity.py | Python | gpl-3.0 | 5,229 | [
"DIRAC"
] | b39d2512f4e2efd4aa020f45897e04af54db72f1811f76dff160d0de4d1e28aa |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | psi4/psi4 | psi4/header.py | Python | lgpl-3.0 | 3,388 | [
"Psi4"
] | 5fe033778a11b0803a814a3b4e906732bb0de2943d87c920476dcbdb02b8b121 |
# Copyright 2019 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | ghchinoy/tensorflow | tensorflow/python/keras/layers/kernelized.py | Python | apache-2.0 | 11,044 | [
"Gaussian"
] | fc1c5b0e97069ab4217652c1258d692955564ae82a1ae4a3087342d18604f5b7 |
# Copyright 2014-2017 CERN. This software is distributed under the
# terms of the GNU General Public Licence version 3 (GPL Version 3),
# copied verbatim in the file LICENCE.md.
# In applying this licence, CERN does not waive the privileges and immunities
# granted to it by virtue of its status as an Intergover... | blond-admin/BLonD | __EXAMPLES/main_files/EX_13_synchrotron_radiation.py | Python | gpl-3.0 | 10,317 | [
"Gaussian"
] | 18f5a64b714aa171108789bf8633e6f8fe756ecde9085e9168b45469251a2dc6 |
# will ``sample_submission`` to your submission filename.
from sample_submission import regressor
import numpy as np
def rmse(a, b):
"""
This function produces a point-wise root mean squared error error between ``a`` and ``b``
Args:
a: first input ndarray
b: second input ndarray
Retu... | WenboTien/Machine_Learning_prac | project1/tiny1/test_script.py | Python | mit | 3,231 | [
"Gaussian"
] | d21436b48a1a3374c9dd6d69b2015a03819ca54f3be02ce2b8cd2408c3854de2 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | lgarren/spack | var/spack/repos/builtin/packages/r-multtest/package.py | Python | lgpl-2.1 | 1,752 | [
"Bioconductor"
] | 8d971809999cb7af74bef9f05dc66fddbb4cd27735f71ac8c087554df27aed98 |
""" EmailAgent
This agent reads the ResourceStatusCache table of ResourceStatusDB
for sending emails with aggregated information about state changes,
and then clears it.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN EmailAgent
:end-before: ##END
:dedent: 2
:caption: EmailAgent options
"... | ic-hep/DIRAC | src/DIRAC/ResourceStatusSystem/Agent/EmailAgent.py | Python | gpl-3.0 | 6,111 | [
"DIRAC"
] | db77c47c1e907cd8363f581eb1d59baf33fe872533ed611b2b710b383b86524d |
#!/usr/bin/env python
# 26.09.2006, c
import os.path as op
from optparse import OptionParser
import init_sfepy
from sfepy.base.base import *
from sfepy.fem.mesh import Mesh
from sfepy.fem.meshio import HDF5MeshIO
from sfepy.solvers.ts import TimeStepper
from sfepy.base.ioutils import get_trunk, write_dict_hdf5
##
# ... | certik/sfepy | extractor.py | Python | bsd-3-clause | 6,130 | [
"VTK"
] | ce41e16596bc4c66d6557a9cc34c4bc9d64aafc615ea8659a7849d764f5e998b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import pylid
from collections import Counter
hmn = pylid.PyLID(3)
hmn.total_ngrams = 159771623
hmn.lang = 'hmn'
hmn.ngrams = Counter({
u' ts': 1396157,
u'ab ': 1298229,
u'as ': 1253541,
u'is ': 1205135,
u's t': 1203015,
u'aj ': 1159263,
u'og ':... | dmort27/pylid | pylid/langs/hmn.py | Python | mit | 773,284 | [
"ASE",
"BWA",
"CDK",
"EPW",
"Elk",
"MOE",
"VMD"
] | 9d5eeffe6a0d07a02022447797e0e5d6c3eb3644ee8a21791b3a28b0eb2e0f70 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2005-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2012 Tim G L Lyons
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publ... | arunkgupta/gramps | gramps/plugins/import/importgrdb.py | Python | gpl-2.0 | 2,858 | [
"Brian"
] | b24bd994a044c8b10943bd5d08db89456e50c493ca3b06a18c1b88e50885871c |
#!/usr/bin/env python3
# -*- coding: UTF-8 -*-
"""This module contains a collection of printing functions for this package."""
import numpy as np
import sys
TAB = " " * 2
def print_complex(np_complex, scaling=1.0, precision=6):
"""Return a string of a (numpy) complex number."""
freq_f = "{{0:> {},.{}f}}".f... | jdcapa/MolecularToolbox | moleculartoolbox/printfunctions.py | Python | gpl-3.0 | 13,523 | [
"CFOUR"
] | ef807e5a1ab090999fdae3f88d88816521ace479a5fe1a0a82a0e80ca15b629f |
"""
Double ring model
References:
Ardid, Wang, Compte 2007 Journal of Neuroscience
doi: 10.1523/JNEUROSCI.1145-07.2007
How is the long-range connection modeled?
"""
from __future__ import division
from collections import OrderedDict
from scipy.signal import fftconvolve
import scipy.stats
import random as pyrand # Im... | xjwanglab/book | ardid2007/ardid2007.py | Python | mit | 16,728 | [
"Brian",
"NEURON"
] | 3b7f896a0630efa12156bb4e1326d043f6b59546fea6c682a0fdbb93e48f07b0 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# ePuck.py
#
# Copyright 2010 Manuel Martín Ortiz <manuel.martin@itrblabs.eu>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either v... | FlorianNaumann/ePuck_Sercom_cpp | ePuck.py | Python | gpl-3.0 | 25,529 | [
"VisIt"
] | 42eec46babb73f549fe2af378a36b6efc8f35f335eb47da2467e456b018a08af |
__author__ = 'Robert Meyer'
from brian import *
def run_network():
clear(True, True)
monitor_dict={}
defaultclock.dt= 0.01*ms
C=281*pF
gL=30*nS
EL=-70.6*mV
VT=-50.4*mV
DeltaT=2*mV
tauw=40*ms
a=4*nS
b=0.08*nA
I=8*nA
Vcut=DeltaT# practical threshold condition
N... | nigroup/pypet | pypet/tests/unittests/briantests/run_a_brian_network.py | Python | bsd-3-clause | 2,219 | [
"Brian",
"NEURON"
] | 25862f9f60803512f525046197082bc2f611014daf690ee7c50968eec3fed86f |
#!/usr/local/bin/python
#CHIPSEC: Platform Security Assessment Framework
#Copyright (c) 2010-2015, Intel Corporation
#
#This program is free software; you can redistribute it and/or
#modify it under the terms of the GNU General Public License
#as published by the Free Software Foundation; Version 2.
#
#This pr... | raisfathin/chipsec | source/tool/chipsec/hal/pcidb.py | Python | gpl-2.0 | 393,089 | [
"BWA",
"CRYSTAL",
"Octopus",
"VisIt"
] | 5302928a7965b4f28dcab1f83c42dfa228176a67a962494455d9f6c0c0c547e5 |
"""
docstring needed
:copyright: Copyright 2010-2017 by the NineML Python team, see AUTHORS.
:license: BSD-3, see LICENSE for details.
"""
from nineml.exceptions import NineMLUsageError
from nineml.visitors import BaseVisitor
# Check that the sub-components stored are all of the
# right types:
class LocalNameConfli... | INCF/lib9ML | nineml/abstraction/componentclass/visitors/validators/names.py | Python | bsd-3-clause | 2,958 | [
"VisIt"
] | 0f9d0c495722ef37ef43e05ee7aedbb5b7d7cef1acaeee91c9807abae1a46150 |
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